These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Moral Event Horizon: Cipher as a whole crosses it in the first scene (as if they weren't on the other side of the line already) with the destruction of the S.S. Libra, which is confirmed to kill several people.
Individually, we have Snattle's imprisonment of an entire town's population (apparently using violence no less), Lovrina's corruption of Shadow Lugia, and Ardos attempting to get Michael and everyone else within the area killed.
Paranoia Fuel: In XD, Cipher Peons have a tendency to drop down from the ceiling when you least expect it. There's also one time where you get on an elevator alone, and you come out of said elevator with a Peon behind you.
Scrappy Mechanic: Poke Spots defeated the entire point of Shadow Pokemon and Orre.
Though a Poke Spot had three different Pokemon each to catch for a total of nine with three Poke Spots, and even then, three were necessary to trade for Duking's Meditite, Shuckle, and Larvitar, making it a total of just twelve different kinds by using the Poke Spots.
Greevil not only has access to the three Legendary Birds, but also Lugia, as well as three Pokemon that are fairly strong in their own right.
Snattle's 2nd fight isn't Greevil-caliber, but it's also fairly brutal on its own, mainly due to his Shadow Starmie being a decent sweeper and being fought a long way away from a healing machine on either end, but you fight the smartest grunt in the franchise right afterwards.
Eldes. His Shadow Salamence is a few levels higher than anything you've fought at this point, and it will steamroller anything that isn't a Shadow Pokémon. Not only that, but his other Shadow Pokémon hit quite hard as well.
They Changed It, Now It Sucks: The things they didn't keep the same rubbed some fans the wrong way, particularly changing Orre into a much more habitable place, thus losing its "edge."